User-friendly RNA-Seq analysis tools designed for biologists

RNA Sequencing Data Analysis Solutions

Once the domain of bioinformatics experts, RNA sequencing (RNA-Seq) data analysis is now more accessible than ever. Illumina offers push-button RNA-Seq software tools packaged in intuitive user interfaces designed for biologists.

These user-friendly tools support a broad range of next-generation sequencing (NGS) studies, from gene expression analysis to total RNA expression profiling and more.

Intuitive Analysis of RNA-Seq Data

RNA-Seq data can be instantly and securely transferred, stored, and analyzed in BaseSpace Sequence Hub, the Illumina genomics cloud computing platform. In addition, the Illumina DRAGEN Bio-IT Platform provides accurate, ultra-rapid secondary analysis of RNA-Seq and other NGS data, in BaseSpace Sequence Hub or on-premise. Our RNA-Seq analysis apps are:

  • Accessible to any researcher, regardless of bioinformatics experience
  • An expert-preferred suite of RNA-Seq software tools, developed or optimized by Illumina or from a growing ecosystem of third-party app providers
  • Designed to support common transcriptome studies, from gene expression quantification to detection of novel transcripts, coding single nucleotide polymorphisms (cSNPs), gene fusions, and more
  • Suitable for human, mouse, and rat RNA-Seq analysis (certain apps support additional species)
  • Compatible with all Illumina sequencing systems

Learn more about:

BaseSpace Sequence Hub

DRAGEN Bio-IT Platform

RNA-Seq Data Analysis FAQs

Demystifying RNA sequencing data analysis with answers to common questions and concerns.

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The BRC-Seq core sequencing facility at the University of British Columbia uses BaseSpace Sequence Hub to analyze and share data. Their studies frequently involve analysis of mRNA sequencing data to assess the impact of different experimental treatments on the transcriptome. The BaseSpace workflow helps BRC-Seq track samples and deliver high-quality sequencing data to its customers.

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BRC-Seq Customers Benefit from Streamlined BaseSpace Workflow

Key RNA-Seq Analysis Apps

Based on frequently cited RNA-Seq analysis pipelines, these apps support a broad range of transcriptome data analysis needs.


COVID-19 Software

Accelerate SARS-CoV-2 RNA detection and identification, perform host response studies, simplify your sample tracking, and contribute to public databases, free of charge.

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SARS-CoV-2 NGS Data Toolkit

Walk through a typical BaseSpace Sequence Hub RNA sequencing data analysis workflow. Learn how to analyze your results, and view examples of the easily interpretable tables and graphs that the software generates.

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After data analysis, results can be transferred easily to BaseSpace Correlation Engine for functional annotation, to understand the biological effects of gene expression changes. BaseSpace Correlation Engine contains data sets from thousands of public studies that inform biological interpretation. Connect differential gene expression data from RNA-Seq experiments with disease associations, or visualize correlated genes and microRNA targets.

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Simplifying Genomic Data Mining

Learn how BaseSpace Correlation Engine facilitates genomic data interpretation. See examples of distinguished universities and pharmaceutical companies that have cited this tool in peer-reviewed publications.

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Tale of Two RNA Library Prep Kits
A Tale of Two RNA Library Prep Kits

Comparative RNA-Seq data analysis from two TruSeq RNA kits revealed key differences in variant and fusion detection.

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